config.yaml

name: 'quickbind_default'
seed: 1
num_epochs: 500 
batch_size: 1
patience: 50
iters_to_accumulate: 2
loss_params:
  lig_lig_loss_weight: 1
  lig_rec_loss_weight: 1
  aux_loss_weight: 1
  steric_clash_loss_weight: 1
  full_distogram_loss_weight: 0

train_names: 'data/timesplit_no_lig_overlap_train'
val_names: 'data/timesplit_no_lig_overlap_val'
test_names: 'data/timesplit_test'
num_workers: 4
dataset_params:
  chain_radius: 10 # only keep chains that have an atom in this radius around the ligand
  remove_h: True
  cropping: True
  crop_size: 256
  binding_site_cropping: True
  recenter: True

optimizer: AdamW
optimizer_params:
  lr: 1.0e-4
  weight_decay: 1.0e-4
clip_grad: 100 # leave empty for no grad clip

model_parameters:
  recycle: False
  recycle_iters: 1
  c_emb: 32
  c_s: 64
  c_z: 64
  c_hidden: 16
  no_heads: 12
  no_qk_points: 4
  no_v_points: 8
  num_struct_blocks: 8
  dropout_rate: 0.1
  no_transition_layers: 1
  share_ipa_weights: True
  c_hidden_msa_att: 16 # c_s // 4 
  c_hidden_opm: 16 # c_z  // 4
  c_hidden_mul: 64 # c_z
  c_hidden_pair_att: 16 # c_z // 4
  c_s_out: 64
  no_heads_msa: 8
  no_heads_pair: 4
  no_evo_blocks: 12
  opm_first: False
  transition_n: 4
  msa_dropout: 0.15
  pair_dropout: 0.25
  use_pairwise_dist: True
  use_radial_basis: False
  use_rel_pos: True
  mask_off_diagonal: True
  use_op_edge_embed: False
  use_gated_ipa: True
  communicate: False
  one_hot_adj: False
  use_full_evo_stack: True
  att_update: True
  use_multimer_rel_pos: False
  use_topological_distance: False
  construct_frames: True
  
wandb:
  project: 'QuickBind'
  resume: allow